title: Mouse neonate thymocytes, Mock infected

city: Saint Louis

first: Andrei

last: Belean

state: Missouri

address: 4939 Children’s Place

department: IM-Rheumatology

institute: Washington University in Saint Louis

data_processing:
Cell Ranger v3.1.0 Pipeline
Assembly: A custom refernce genome combining GRCm38 with the murine roseolovirus genome
Supplementary files format and content: compressed tab-delimited text file contains raw counts
Supplementary files format and content: compressed tab-delimited text file contains barcodes
Supplementary files format and content: compressed tab-delimited text file contains features

source_name: Thymus

extract_protocol:
The thymus was dissected with care to remove non-thymic tissue using scissors. The thymus tissue was placed into 1ml of 0.25% trypsin EDTA (GIBCO) at 37ºC. The tissue was incubated for 15 minutes. Dissociation and digestion were aided by vigorous pipetting using a large bore pipette every 5 minutes. Cells were filter through a 100μm filter into 9ml of RPMI 10% FBS to neutralize trypsin activity. Cells were then centrifuged at 1500rpm for 3.5 minutes followed by incubation in RBC lysis buffer (made in house) for 3 min at room temperature. Cells were then centrifuged again and washed twice in 9ml of PBS 0.5% bovine serum albumin (BSA). Cells were counted via hemocytometer then resuspended at 1200 cells/μL in PBS 0.04% BSA. The cells were kept on ice until ready for scRNAseq analysis.
Single-cell 3’ gene expression cDNA libraries were generated per manufacture protocols using the 10X Genomic Chromium Single-Cell 3’ Library and Gel Bead Kit v1 and the 10x Chromium Controller

value: Thymus

value: neonate thymocytes

value: mock (saline) infected


title: AB_15_1

status: Public on May 17 2024

type: SRA

city: Hangzhou

first: Bin

last: Yang

email: rayyangbin@163.com, binyang@zju.edu.cn

state: Zhejiang

address: No. 866 Yuhangtang Road

department: College of Animal Sciences

country: China

institute: Zhejiang University

description: tissue transcriptomic data

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.4.
TopHat2 (v2.0.13) with Bowtie2 (v2.3.3.1) was used to align the high-quality reads to the sheep reference genome (Ovis aries v3.1).
The BAM alignment files that were generated from TopHat2 were sorted by name and converted into SAM files using Samtools (v1.1).
HTSeq-count (v0.9.1) was used to count the number of reads per gene with the SAM files based on the annotation files.
Assembly: Ovis aries v3.1
Supplementary files format and content: Sample was represented by tab-delimited text files including raw counts of each gene for each sample.

molecule: total RNA

organism: Ovis aries

source_name: Abomasum epithelium

growth_protocol: Normal feeding and management on commercial farm.

extract_protocol:
Total RNA were extracted using a total RNA extraction kit (Aidllab, Beijing, China) according to the instructions. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). All the RNA samples had integrity greater than 9.
RNA samples were subjected to cDNA library construction using the NEBNext UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s recommendations.

tag: tissue

value: Abomasum epithelium

tag: age

value: 15 days of age

tag: gender

value: male

tag: strain

value: Hu sheep


title: scRNA-seq_P130

city: Beijing

first: Yuxuan

last: Sun

address: Yiheyuan Road

institute: Peking University

description:
10X Genomics
Real/RWC

library_source: transcriptomic single cell

data_processing:
The generated scRNA-seq data were aligned and quantified using the Cell Ranger Single-Cell toolkit (version 6.1.2), employing GRCh38 as the reference genome. The preliminary filtered data generated from Cell Ranger were used for downstream analysis. The TCR sequence data from 10X Genomics was processed using Cell Ranger software (version 6.1.2) with the manufacturer-supplied human VDJ reference genome.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

organism: Homo sapiens

source_name: lung

extract_protocol:
Fresh tumor tissues were cut into pieces of approximately 1mm3 in the RPMI-1640 medium (Gibco, 11875093) with 10% fetal bovine serum (FBS; Gibco, 10099141), and enzymatically digested with Tumor Dissociation Kit (Miltenyi, 130-095-929) for 60 minutes on a rotor at 37 °C. Dissociated cells were subsequently passed through a 100μm MACS SmartStrainers (Miltenyi, 130-110-917) and centrifuged at 300g for 8 minutes. After removing supernatant, the pelleted cells were suspended in red blood cell lysis buffer (TIANDZ, 90309-100) and incubated on ice for 5 minutes to lyse red blood cells. After washing with PBS (Gibco, 10010023), cell pellets were re-suspended in sorting buffer (PBS supplemented with 2% FBS). Single-cell suspensions were then stained with 7-AAD Viability Staining Solution (Invitrogen, 00-6993-50) and an antibody against CD235a (BioLegend, 349114) for FACS sorting on a BD Aria III instrument. Non-erythrocytic living cells were enriched by gating 7AAD−CD235a− cells. The concentration of single-cell suspensions was then adjusted to 700~1,200 cells μl–1 and single-cell suspensions with viable cell rate greater than 80% were used for single cell sequencing.
In total, ~18,000 cells for each sample were used for 10X Chromium Single cell 5′ and human TCR library construction (10X Genomics), according to the manufacturer’s instructions. All subsequent steps were performed following the standard manufacturer protocols. Purified libraries were subsequently sequenced using an Illumina NovaSeq 6000 sequencer with 150-base pair (bp) paired-end reads.

value: lung


title: Mouse neonate thymocytes, MRV infected

country: USA

molecule: polyA RNA

organism: Mus musculus

tag: cell type

tag: treatment

value: murine roseolovirus infected


title: Canine adipose-derived mesenchymal stem cells - biological replicate 6 - condition uninfected

type: RNA

city: Zagreb

first: Marina

last: Prišlin

address: Savska cesta 148

department: Virology Department

country: Croatia

institute: Croatian Veterinary Institute

description: Control Group

data_processing:
Following data acquisition, normalization, and in-depth analysis were conducted using the specialized RT2 Profiler PCR Array Data Analysis software, accessible online at https://dataanalysis2.qiagen.com/pcr (accessed November 10th, 2023). For the normalization it uses the average of five housekeeping genes: B2M, HPRT1 , RPL13A, PGK1, ACTB. The statistical significance was calculated based on a Student’s t-test of the replicate 2^ (- Delta CT) values for each gene in the control and treatment groups. The software automatically appointed a fold change cutoff of 2.0, equal to log2Fold Change ± 1.0.
Fold Change worksheet reports test/control (CHV-infected/uninfected) ratios.

label: SYBR Green

organism: Canis lupus familiaris

source_name: Isolated and in vitro cultured adipose tissue cells

label_protocol: Genomic DNA elimination and complementary DNA synthesis from 800 ng of RNA was accomplished using the RT2 First Strand kit (Qiagen, Cat. 330401) as instructed by the manufacturer. Subsequently, a commercially available RT² Profiler™ PCR Array for Dog Mesenchymal Stem Cells (PAFD-082ZR, Qiagen) with SYBR Green-optimized primer assays (Qiagen, Cat. 330603) was applied, following the manufacturer's instructions for Rotor-Gene Q (Qiagen). The array featured primers targeting 84 genes, categorized as stemness markers, MSC-specific, MSC-associated, and MSC-differentiation genes associated with osteogenesis, adipogenesis, chondrogenesis, myogenesis, and tenogenesis.

growth_protocol: The extraction of cAD-MSCs was carried out within a two-hour window from sample collection. This process involved rinsing and cutting the adipose tissue with a scalpel, followed by enzymatic digestion using 0.5% collagenase type 1 (Gibco, Cat. 17100017). The obtained stromal vascular fraction was subsequently placed into T25 cell culture flasks (Nunc, Thermo Fisher Scientific) and cultured in basal media comprising 79% Dulbecco's Modified Eagle Medium with Low Glucose (DMEM Low Glucose) (Gibco, Cat. 31885049), 20% Fetal Bovine Serum (FBS) (Gibco; Cat. 1027010), and 1% Penicillin/Streptomycin (Sigma-Aldrich, Cat. P4333-100ML) at 37°C. Media was replaced after 24 hours, and when adherent cells reached 90% confluence, subculturing was performed using a solution of 0.05% Trypsin and 0.02% EDTA (Sigma-Aldrich, Cat. 59417C-500ML) until proliferation arrest was observed.

extract_protocol: Gene expression analysis using an RT-qPCR array was conducted following total RNA extraction in two conditions during in vitro culture, uninfected and canine herpesvirus (CHV) infected samples. The cAD-MSCs reached approximately 90% confluence in T75 cell culture flasks (Nunc, Thermo Fisher Scientific). Subsequently, the cells were detached using a cell scraper (Nunc, Thermo Fisher Scientific) and centrifuged at 235× g for 10 minutes. Total RNA extraction was performed using the RNeasy Mini Kit (Qiagen, Cat. 74106) with 2M dithiothreitol (Sigma-Aldrich, Cat. 43815-1G), following the manufacturer's instructions. The extracted RNA was stored at -80°C until gene expression analysis.

tag: Sex

value: female

tag: agent


title: scRNA-seq_P122

description:
10X Genomics
Real/RWC


title: FP_Old_4

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

data_processing:
BCL files were de-multiplexed and converted to FASTQ files using bcl2fastq program (v2.20.0.422).
FASTQ files were trimmed for adapters using BBduk tool version 38.76, and aligned to mouse genome Mus_musculus_MM10_NCBIM38_89 with STAR software v2.7.0f_0328.
featureCounts from R package Subread (version 2.10.5) was used to generate gene counts.
Differential expression analysis of gene counts was performed using the DESeq2
Assembly: mm10
Supplementary files format and content: text files containing counts

source_name: Fore footpad skin from 28 months old wild-type mouse

extract_protocol:
Footpad skin from fore paws of 3 months old and 28 months old C57BL/6JN male mice were isolated under a dissection microscope.  Total RNA was isolated using Qiagen RNeasy Fibrous Tissue Mini Kit (Qiagen Cat# 74704).  The quality and quantity of RNA were checked with Agilent Bioanalyzer using RNA 6000 Nano Kit (Agilent Cat# 5067-1511).
Total RNA was used for sequencing library prep using Illumina TruSeq Stranded mRNA Library prep kit (Illumina Cat# 20020594).  Briefly, the Poly-A containing mRNA was isolated first by using Poly-T oligo attached magnetic beads.  After cDNA synthesis, the cDNAs were subjected to the 3’ End Adenylation, the Adapter Ligation, and purified with AMPure beads (Beckman, Cat#A63881).  The products were size selected with SPRIselect beads (Beckman, Cat#B23318).  Then selected cDNAs were enriched by PCR and purified again with SPRIselect beads to generate final libraries.  The quality and quantity of sequencing libraries were checked using Agilent DNA 1000 Screen Tape on the Agilent Tapestation.

value: Male

value: 28 months

value: Fore footpad skin

tag: genotype

value: wild-type


title: OM_15_3

description: tissue transcriptomic data

source_name: Omasum epithelium

value: Omasum epithelium


title: Canine adipose-derived mesenchymal stem cells - biological replicate 5 - condition uninfected

description: Control Group


title: RU_25_1

description: tissue transcriptomic data

source_name: Rumen epithelium

value: Rumen epithelium

value: 25 days of age


title: Canine adipose-derived mesenchymal stem cells - biological replicate 3 - condition uninfected

description: Control Group


title: Canine adipose-derived mesenchymal stem cells - biological replicate 4 - condition uninfected

description: Control Group


title: OM_15_2

description: tissue transcriptomic data


title: scRNA-seq_P64

description:
10X Genomics
Real/RWC


title: FP_Old_3


title: OM_15_1

description: tissue transcriptomic data


title: scRNA-seq_P105

description:
10X Genomics
Real/RWC


title: RE_15_3

description: tissue transcriptomic data

source_name: Reticulum epithelium

value: Reticulum epithelium


title: scRNA-seq_P70

description:
10X Genomics
Real/RWC


title: FP_Old_2


title: FP_Old_1


title: Canine adipose-derived mesenchymal stem cells - biological replicate 2 - condition uninfected

description: Control Group


title: RE_15_2

description: tissue transcriptomic data


title: Canine adipose-derived mesenchymal stem cells - biological replicate 1 - condition uninfected

description: Control Group


title: FP_Young_4

source_name: Fore footpad skin from 3 months old wild-type mouse

value: 3 months


title: FP_Young_3


title: scRNA-seq_P52

description:
10X Genomics
Real/RWC


title: FP_Young_2


title: scRNA-seq_P591

description:
10X Genomics
IIT


title: RE_15_1

description: tissue transcriptomic data


title: scRNA-seq_P590

description:
10X Genomics
IIT


title: Brionchial epithelial tissue, normal-like model, untreated, replicate 2_S13

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

country: Germany

institute: Berlin Institute of Health, Charité Medical University of Berlin

data_processing:
Reads were demultiplexed using Illumina's BCL Convert and mapped to the genome using using the STAR aligner, v. 2.7.8.a.
For quality control, we used FastQC and MultiQC.
Read counts were collected using featureCounts. Features with fewer than a total of 10 counts or fewer than 5 samples with at least 3 counts were eliminated.
For differential gene expression analysis, we used the R package DESeq2, v. 1.30.1. Gene set enrichment testing was done with the CERNO algorithm implemented in the tmod package, v. 0.50.7.
with gene sets sourced from the MSigDB using the msigdbr package, v. 7.4.1.
Assembly: GRCh38, p7
Supplementary files format and content: tab-delimited text file containing raw counts for all samples

source_name: Brionchial epithelial tissue

growth_protocol: We developed a microfluidic two-organ chip setup which contained an atopic-like skin disease model that was co-cultivated with a 3D bronchial epithelial tissue model over four days on a dynamic organ chip platform that ensured media circulation and flow from the skin to the healthy lung tissue (Fig. 6 a, b). Activated CD4+ T cells were added to the circuit due to their role as direct TSLP effector cells

extract_protocol:
the total RNA was isolated using the Invitrogen PureLink™ RNA Mini Kit (ThermoFisher, Burnaby, BC, Canada) according to the manufacturer’s protocol.
Sample quality control was performed using the Agilent 2100 Bioanalyzer or the Agilent 4200 TapeStation. Qualifying samples were then prepped following the standard protocol for the Illumina Stranded mRNA prep (Illumina).

treatment_protocol: BP79 was topically applied onto the atopic-like skin disease models once every 24 h over 4 days.

value: Brionchial epithelial tissue

tag: treatment 1

value: normal-like model

tag: treatment 2

value: untreated

tag: replicate


title: Skin tissue, normal-like model, untreated, replicate 2_S7

source_name: Skin tissue

value: Skin tissue


title: scRNA-seq_P33

description:
10X Genomics
Real/RWC


title: RU_15_2

description: tissue transcriptomic data

value: 15 days of age

value: male

value: Hu sheep


title: scRNA-seq_P589

description:
10X Genomics
IIT

value: lung


title: FP_Young_1

value: Male


title: RU_15_3

description: tissue transcriptomic data


title: Brionchial epithelial tissue, normal-like model, untreated, replicate 1_S12


title: TA_FP_3

data_processing:
BCL files were de-multiplexed and converted to FASTQ files using bcl2fastq program (v2.20.0.422).
FASTQ files were trimmed for adapter sequences using Cutadapt version v1.18 and aligned to mouse genome mm10, Ensembl v89 using STAR software v2.4.0j.
featureCounts (v1.6.4) were used to generate gene counts
Differential expression analysis of gene counts was performed using the DESeq2
Assembly: mm10
Supplementary files format and content: text files containing counts

source_name: Fore footpad skin 3 months old Eda mutant Tabby mouse

extract_protocol:
Footpad skin from fore paws of 3 months old Eda mutant Tabby male mice and age and sex matched C57BL/6J control mice was collected under a dissection microscope.  Total RNA was isolated using Qiagen RNeasy Fibrous Tissue Mini Kit (Qiagen Cat# 74704).  The quality and quantity of RNA were checked with Agilent Bioanalyzer using RNA 6000 Nano Kit (Agilent Cat# 5067-1511).
Total RNA was used for sequencing library prep using Illumina TruSeq Stranded mRNA Library prep kit (Illumina Cat# 20020594).  Briefly, the Poly-A containing mRNA was isolated first by using Poly-T oligo attached magnetic beads.  After cDNA synthesis, the cDNAs were subjected to the 3’ End Adenylation, the Adapter Ligation, and purified with AMPure beads (Beckman, Cat#A63881).  The products were size selected with SPRIselect beads (Beckman, Cat#B23318).  Then selected cDNAs were enriched by PCR and purified again with SPRIselect beads to generate final libraries.  The quality and quantity of sequencing libraries were checked using Agilent DNA 1000 Screen Tape on the Agilent Tapestation.

value: Tabby

value: Eda mutant


title: scRNA-seq_P586

description:
10X Genomics
IIT


title: RU_15_1

description: tissue transcriptomic data


title: Skin tissue, atopic-like model, untreated, replicate 1_S8

value: atopic-like model


title: Skin tissue, atopic-like model, untreated, replicate 2_S9


title: Skin tissue, normal-like model, untreated, replicate 1_S6


title: TA_FP_1

value: Fore footpad skin


title: WT_FP_3

source_name: Fore footpad skin 3 months old wild-type mouse

value: Wild-type


title: scRNA-seq_P549

description:
10X Genomics
IIT


title: WT low dose LPS neutrophil

city: Blacksburg

first: Liwu

last: Li

state: VA

address: 1015 Life Science Cir

institute: Virginia Tech

data_processing:
Cellranger 3.1.0 version
All the data were merged using Seurat's integration workflow. The merged data was then saved in RDS format using the "saveRDS" function.
Assembly: mm10
Supplementary files format and content: Seurat RDS (gz file with matrix can be read by Seurat)

source_name: neutrophil

growth_protocol: Murine bone marrow neutrophils were purified by the percoll gradient method, and cultured in complete RPMI medium (10% fetal bovine serum, 2 mM L-glutamine, and 1% penicillin/streptomycin) supplemented with 1 ng/ml GM-CSF.

extract_protocol:
cDNA libraries were generated from treated cells by using the 10X Genomics Chromium Single Cell 3' Reagent Kits (version 3 Chemistry)
Single-cell suspensions were loaded onto the Chromium Controller to generate 1,000 single-cell gel beads in emulsion per sample. The cDNA of each sample after amplification of 12 cycles was quantified by Qubit and quality-checked by Bioanalyzer to verify the size distribution of cDNA samples and determine indexed PCR amplification of 15 cycles to yield a sufficient and unbiased library for sequencing. After library quality control by Tapestation, indexed library samples were quantified by KAPA library quantification kit (Universal) and pooled with 15 ul of 5 nM for each sample.
Libraries were pooled togegther for sequencing on Illumina Hiseq4000

treatment_protocol: Cultured bone marrow neutrophils from WT and TRAM knockout mice were treated with PBS or 100 pg/ml LPS for 24 h.

value: WT

value: BM-derived neutrophil

tag: stimulated by

value: GM-CSF

value: LLPS


title: WT PBS neutrophil

value: PBS


title: hCEnCs, UVA_3

city: Kyoto

first: Kohsaku

last: Numa

state: Kyoto

address: 465 Kajii-cho, Kawaramachi-Hirokoji, Kamigyo-ku

department: Department of Ophthalmology

country: Japan

institute: Kyoto Prefectural University of Medicine

data_processing:
initial quality assessment of raw RNA-seq data was performed using FastQC (v0.12.1) to evaluate read quality.
TrimGalore (v4.3) was conducted to remove adapter sequences, and low-quality reads.
The trimmed reads were aligned to the reference genome (GRCh38) using HISAT2 (v2.2.1).
We converted the output SAM files to sorted BAM files with SAMtools (v1.12) for downstream analysis.
FeatureCounts (v2.0.3) was utilized to assign mapped reads to their corresponding genes, generating count data for each gene.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: raw count data for each sample

source_name: Cornea

extract_protocol:
ISOLATE II RNA Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Cornea

tag: cell line

value: Primary

value: corneal endothelial cell

value: UVA

value: UVA exposure


title: hCEnCs, UVA_4


title: TA_FP_2

value: 3 months


title: scRNA-seq_P531

description:
10X Genomics
IIT

value: lung


title: WT_FP_2

value: Male


title: WT_FP_1


title: hCEnCs, UVA_2


title: Brionchial epithelial tissue, atopic-like model, untreated, replicate 2_S8

value: Brionchial epithelial tissue

value: untreated


title: hCEnCs, UVA_1


title: scRNA-seq_P529

description:
10X Genomics
IIT


title: 3rG4 cl6 k27me3 rep2 input

city: Boston

first: yongwoo

last: lee

state: MA

address: 185 Cambridge St

department: Mol bio

institute: MASSACHUSETTS GENERAL HOSPITAL

library_source: genomic

data_processing:
Adaptor sequences and PCR duplicates are removed from the raw read files. For Xi (mus) and Xa (cas) allelic analysis, adaptor trimmed total sequencing reads were allele-specifically aligned to 129S1/SvJm (mus) and CAST/Eih (cas) genomes. FPM and input normalized BigWig track files are generated for visualization and further quantification of H3K27me3 density on the different gene groups. mm10 bigwig files were created using the UCSC tool LiftOver from mm9 aligned bigwig files
Assembly: mm9
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: Day 7 differentiated mouse embryonic stem cells

growth_protocol: Clonal TsixTST/+  mESC (TST) line was cultured as routine procedure. mESC were grown on inactivated feeders in high glucose D-MEM supplemented with 15% Hyclone FBS, 25 mM HEPES pH 7.2-7.5, 1x MEM non-essential amino acids, 1x Pen/Strep, 0.1 mM βME, and 500 U/mL ESGRO recombinant mouse Leukemia Inhibitory Factor (LIF) protein at 37°C with 5% CO2. EB differentiation was performed with growing feeder-depleted cells in the medium without LIF. Cells were kept in suspension until 3 days of differentiation and transferred to gelatinized plates on day 3 for further adherent growth.

extract_protocol:
10 million cells per ChIP were resuspended with 0.5 ml ice-cold ChIP lysis buffer (50 mM Tris-HCl pH8, 10 mM EDTA pH8, 1% SDS).  Cell extracts were subjected to sonication using the Qsonica apparatus (40% power, 30s on/ 30s off for total sonication time 30 min at 4°C). Sheared chromatin was checked on the 1% agarose gel electrophoresis, repeat sonication a second time if the fragment is larger than 1 kb marker. 0.1 ml lysate was mixed with 1.2 ml ChIP dilution buffer (20 mM Tris-HCl pH8, 150 mM NaCl, 1% Triton X-100, 2 mM EDTA pH8), and incubated with 2 μg antibody for overnight at 4°C. Immunoprotein complex was captured with 20 μL Dynabeads Protein G for 5 hr incubation. Afterward, beads were washed three times with ChIP wash buffer 1 (20 mM Tris-HCl pH8, 150 mM NaCl, 2mM EDTA pH8, 1% Triton X-100, 0.1% SDS) and once with ChIP wash buffer 2 (20 mM Tris-HCl pH8, 500 mM NaCl, 2mM EDTA pH8, 1% Triton X-100, 0.1% SDS). 100 μL of ChIP elution buffer (1% SDS, 100 mM NaHCO3, 40 ug/ml RNaseA) was added to the washed bead and incubated for 1hr at 37°C to recover bound nucleoproteins, dynabeads were removed by using magnetic stand. Reverse-crosslinking was done by incubating the supernatant at 65° C overnight.
NEBNext Ultra II DNA Kit (NEB) was used for library preparation by following the product manual.

treatment_protocol: Cells were cross-linked in PBS with 1% formaldehyde at room temp for 20 min with gentle agitation and quenched with 0.125 M glycine for 10 min. Fixed cells were washed twice with PBS, harvested by scraping and stored at -80 °C until use.

value: 129S1/CastEiJ x 129S1

value: Xist 3'rG4 mutant


title: Brionchial epithelial tissue, atopic-like model, untreated, replicate 2_S2

value: atopic-like model


title: hCEnCs, IR_4

value: IR

value: irradiation


title: 3rG4 cl5 k27me3 rep2 input

value: Day 7 differentiated mouse embryonic stem cells


title: scRNA-seq_P438

description:
10X Genomics
IIT


title: Brionchial epithelial tissue, atopic-like model, untreated, replicate 1_S7


title: WT(3rG4) K27me3 rep2 input

value: WT


title: scRNA-seq_P343

description:
10X Genomics
IIT


title: scRNA-seq_P547

description:
10X Genomics
IIT


title: Brionchial epithelial tissue, atopic-like model, untreated, replicate 1_S1


title: Skin tissue, atopic-like model, treated with BP79, replicate 2_S11

value: Skin tissue


title: Osteo-D7

city: Houston

first: Danh

last: Truong

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Seurat was used for quality control analysis, data processing, and visualization.
Assembly: hg38
Supplementary files format and content: Data provided for single-cell RNA-Seq is the raw count matrix HDF5 file from Cell Ranger

source_name: Bone

extract_protocol:
Cells were dissociated from either hydrogels or tissue culture plasticware.
Single-cell rna-sequencing was performed using 10x Genomics Single Cell 3' Gene Expression protocol.

value: Bone

value: Mesenchymal Stem Cell


title: 3rG4 cl6 k27me3 rep1 input


title: hCEnCs, IR_1

value: Cornea

value: Primary

value: corneal endothelial cell


title: hCEnCs, Ctrl_4

value: Control


title: 3rG4 cl5 k27me3 rep1 input


title: Skin tissue, atopic-like model, treated with BP79, replicate 1_S10


title: Osteo-D7_2


title: Brionchial epithelial tissue, atopic-like model, treated with BP79, replicate 2_S10


title: WT(3rG4) K27me3 rep1 input


title: scRNA-seq_P519

description:
10X Genomics
IIT

value: lung


title: Osteo-D5


title: Brionchial epithelial tissue, atopic-like model, treated with BP79, replicate 1_S9

value: Brionchial epithelial tissue


title: Osteo-D3


title: hCEnCs, Ctrl_2

value: untreated


title: hCEnCs, Ctrl_3


title: hCEnCs, IR_3


title: Skin tissue, normal-like model, untreated, replicate R_S51

value: normal-like model


title: 3rG4 cl5 k27me3 rep2

value: 129S1/CastEiJ x 129S1

value: Xist 3'rG4 mutant


title: Brionchial epithelial tissue, atopic-like model, treated with BP79, replicate 1_S3

value: atopic-like model


title: hCEnCs, Ctrl_1


title: Brionchial epithelial tissue, atopic-like model, treated with BP79, replicate 2_S4


title: hCEnCs, IR_2

value: IR

value: irradiation


title: Osteo-D21


title: WT(3rG4) K27me3 rep2

value: Day 7 differentiated mouse embryonic stem cells

value: WT


title: Participant17_V3D0

first: Chamindi

last: Seneviratne

address: 670 W. Baltimore street

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

description: we do not have processed data files

data_processing:
sequencing reads were aligned with the human reference genome GRCh38 using fast splice-aware aligner HISAT2 30 under default parameters to generate the alignment BAM files.
the read alignments were assessed to compute gene expression counts for each gene using the HTSeq count tool
The raw read counts were normalized for  downstream analyses at individual gene and pathway levels, using library size and dispersion of gene expression
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for corresponding samples

source_name: peripheral whole blood

extract_protocol:
Total RNA was extracted from WBC using Macherey-Nagel’s NucleoSpin® miRNA kit and RNA/DNA Buffer kit (Takara Bio USA, Inc. Doral, Fl, USA) according to manufacturer’s guidelines. The RNA integrity was tested using an Agilent bioanalyzer system, and all samples that had an RNA integrity number (RIN) greater than seven were used for sequencing.
Libraries were prepared according to Illumina's instructions
Strand-specific RNAseq

value: peripheral whole blood

value: PBMC

tag: dose

value: HighDose

tag: experimental sequence

tag: study site

value: Female

tag: age (yrs)

tag: plasma etg_(ng/ml)

tag: plasma ets_(ng/ml)

value: Not Detected


title: 3rG4 cl6 k27me3 rep1

tag: strain


title: MZ1-treated HCT116, BRD4 ChIP

city: Maebashi

first: Naoko

last: Hattori

state: Gunma

address: 3-39-15 Showa-mach

department: Institute for Molecular and Cellular Regulation

institute: Gunma University

data_processing:
Fastp (version 0.23.4) was used for sequencing QC and adapter trimming.
All reads were aligned to the human genome GRCh38/hg38 using the short-read aligner Bowtie 2 (version 2.5.1) with default parameters.
The resultant SAM file was converted into a BAM file and duplicates were removed using SAMtools (version 1.18).
Peak calling was performed with the input control using MACS2 (version 2.2.9.1) with default parameters
Assembly: hg38
Supplementary files format and content: bedGraph, narrowPeak (except for  Input samples)

source_name: Colorectal cancer

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. Lysates were clarified from sonicated nuclei and BRD4-histone-DNA complexes were isolated with antibody.
Sequencing library was prepared with GenNext NGS Library Prep Kit (Toyobo, LPK-101) from 5 ng for a final sequencing depth of 50 million reads per sample.

tag: tissue

value: Colorectal cancer

tag: chip antibody


title: Participant16_V3D3

description: we do not have processed data files

tag: cell type

tag: gender

value: Male


title: 3rG4 cl5 k27me3 rep1

tag: genotype


title: PDD00017273-treated HCT116, BRD4 ChIP

tag: treatment


title: 3rG4 cl6 k27me3 rep2


title: Control-HCT116, BRD4 ChIP

value: Control


title: Participant13_V2D0

description: we do not have processed data files


title: MZ1-treated HCT116, Input


title: WT(3rG4) K27me3 rep1


title: Osteo-D2

value: Bone

value: Mesenchymal Stem Cell


title: 3rG4 cl5 D7 RNA rep2

data_processing:
Adaptor sequences were trimmed from the RNA-seq reads.  Sequencing reads were allele-specifically aligned to 129S1/SvJm (mus) and CAST/Eih (cas) genomes using STAR aligner as previously described (Pinter et al., 2012).
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
Total RNA was extracted using TRizol reagent.
oligo dT magnetic beads (NEB) were used for removing abundant rRNA from  Xist 3’ rG4 deletion cells. 50 ng of rRNA depleted RNA was used for RNA-seq library preparation using NEBNext Ultra Directional RNA Library Prep Kit (NEB).

value: 129S1/CastEiJ x 129S1


title: 3rG4 cl6 D7_RNA rep2

value: Xist 3'rG4 mutant


title: PDD00017273-treated HCT116, Input


title: Osteo-D0


title: Control-HCT116, Input


title: Adipo-D7


title: Osteo-D0-5


title: Osteo-D1


title: Brionchial epithelial tissue, normal-like model, untreated, replicate 20220412-R_S52

value: Brionchial epithelial tissue

tag: treatment 1

value: normal-like model

tag: treatment 2

value: untreated


title: 3rG4 cl6 D7_RNA rep1

value: Day 7 differentiated mouse embryonic stem cells


title: Participant1_V2D3

description: we do not have processed data files

value: Placebo


title: Participant16_V2D3

value: peripheral whole blood

value: MediumDose


title: Adipo-D7_2


title: Adipo-D3


title: WT(3rG4) D7 RNA rep2

value: WT


title: 3rG4 cl5 D7 RNA rep1


title: Osteo-D10


title: WT(3rG4) D7 RNA rep1


title: 3rG4_cl6_D7_Xist_CHART rep2 input

data_processing:
CHART-seq reads were aligned allele-specifically to mouse genome using bowtie2 (-p 4 --very-sensitive). Uniquely aliened reads without RCR duplicates were normalized by the number of total aligned reads.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CHART-seq

source_name: 129S1/CastEiJ x 129S1

extract_protocol:
Cell pellets were thawed on ice with 1 ml sucrose buffer (10mM HEPES pH7.5, 0.3M sucrose, 1% Triton X-100, 100mM potassium acetate, 0.1mM EGTA, supplemented with 0.5mM spermidine, 0.15mM spermine, 1mM DTT, 1X Protease Inhibitor Cocktail, 10U/mL SUPERaseIN RNase Inhibitor. Resuspended samples were then homogenized with dounce homogenizer in a volume of 3 ml sucrose buffer. The mixture was layered on a cushion of 7.5ml glycerol buffer (10mM HEPES pH7.5, 25% glycerol, 1mM EDTA, 0.1mM EGTA, 100mM potassium acetate, freshly supplemented with 0.5mM spermidine, 0.15mM spermine, 1mM DTT, 1X PIC, and 5U/mL SUPERaseIN) and centrifugated for 10min in 4C at 1500g. Pellets were resuspended in 3ml 1X PBS and then 3% formaldehyde was added, second fixation was carried out with rotation for 30 min at room temperature. Next, the samples were centrifugated at 1000g for 5min at 4 °C and washed 3 times with ice-cold 1x PBS 0.05% Tween-20. The pellets were resuspended in 1 ml nuclear extraction buffer (50mM HEPES pH 7.5, 250mM NaCl, 0.1mM EGTA, 0.5% N-lauroylsarcosine, 0.1% sodium deoxycholate, 5mM DTT, 10U/mL SUPERaseIN), rotated 10 minutes at 4°C, spinned-down at 400g for 5 minutes at 4C and nuclei were resuspended in 130μl  sonication buffer (50mM HEPES pH 7.5, 75mM NaCl, 0.1mM EGTA, 0.5% N-lauroylsarcosine, 0.1% sodium deoxycholate, 0.1% SDS, 5mM DTT, 10U/mL SUPERaseIN). Sonication was performed with Covaris E220 sonicator at power: 140W, duty factor: 10%, cycles per burst: 200 for 5 minutes at 4C.  The lysate was pre-cleared with addition of Dynabeads MyOne Streptavidin C1 beads (Invitrogen) in 640μl 2X hybridization buffer (50mM Tris-HCl pH 7.0, 750mM NaCl, 1% SDS, 1mM EDTA, 15% formamide, 1mM DTT, 1mM PMSF, 1X PIC, and 100U/mL SUPERaseIN) .  Pre-cleared mixtures received 3.6μl from a 10μM mix of Xist probes and hybridization was performed at room temperature in rotation overnight. Next, 120μl of washed beads were added for each reaction and the tubes were incubated in rotation at 37C for 1 hour. Then beads were washed once with 1X hybridization buffer (33% sonication buffer, 67% 2X hybridization buffer) for 10 min, 5 times with 2% SDS buffer (10mM HEPES pH 7.6, 250mM NaCl, 2% SDS, 2mM EDTA, 2mM EGTA, and 1mM DTT) for 5 min and twice with 0.5% NP40 buffer (10mM HEPES pH7.6, 250mM NaCl, 0.5% NP-40, 3mM MgCl2, and 10mM DTT) for 5min, at 37C. Beads were resuspended with 180μl of 0.5% NP40 buffer and 20μl RNase H (5U/μl, NEB) for 20 minutes in room temperature to elute the DNA twice. Eluted DNA was incubated with RNaseA for 1h at 37C in rotation, following by Proteinase K (20mg/ml) treatment at 55°C 1hr. To reverse crosslinking the DNA, 300 mM NaCl was added to the samples and incubated at 65°C overnight. DNA was extracted with phenol-chloroform extraction.
CHART libraries were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina

treatment_protocol: 25 million cells were crosslinked in 1X PBS with 1% formaldehyde for 10min at room temperature. The formaldehyde was quenched with the addition of 0.125M glycine and rotation for 5min.  Cells were then washed three times with 1x PBS 0.05% Tween-20 and cell pellets were snap freeze in liquid nitrogen.


title: Participant17_V1D0

value: PBMC

value: Female


title: Adipo-D3_2


title: Participant10_V2D0

description: we do not have processed data files

value: HighDose

value: Not Detected


title: Osteo-D14


title: Participant15_V3D0

value: Male


title: Adipo-D1

value: Bone


title: Participant16_V2D0


title: Participant15_V3D3


title: 3rG4_cl5_D7_Xist_CHART rep1 input


title: Participant15_V2D3


title: Adipo-D2

value: Mesenchymal Stem Cell


title: WT_D7_Xist_CHART rep1 input

value: 129S1/CastEiJ x 129S1


title: 3rG4_cl6_D7_Xist_CHART rep1 input

value: Xist 3'rG4 mutant


title: 3rG4_cl5_D7_Xist_CHART rep2 input


title: Adipo-D10


title: Participant15_V2D0


title: Adipo-D0_2


title: 3rG4_cl6_D7_Xist_CHART rep2


title: Participant15_V1D3


title: Adipo-D14


title: Participant14_V1D0


title: Participant15_V1D0


title: Participant14_V1D3


title: Adipo-D0-5


title: Adipo-8H


title: BaF3_ChimP3V3:gp130Box1/2_stimuliert_4

city: Düsseldorf

first: Christiane

last: Seibel

address: Universitätstraße 1

institute: Heinrich-Heine-Universität

data_processing:
After UMI (Unique Molecular Identifier) filtering, all remaining reads of all probes were adapter trimmed and quality trimmed (using the default parameters: bases below Q13 were trimmed from the end of the reads. After grouping of samples (for biological replicates each) according to their respective experimental condition, the statistical differential expression was determined using the Differential Expression for RNA-Seq tool (version 2.7). The resulting pvalues were corrected for multiple testing by FDR correction. A p value of ≤0.05 was considered significant. The Gene Set Enrichment Test (version 1.2) was done with default parameters.
Assembly: Mapping was done against the Mus musculus (mm39; GRCm39.107) genome sequence.
Supplementary files format and content: Excel file

extract_protocol:
mRNA was isolated with NucleoSpin RNA (Macherey-Nagel, Düren, Germany; cat. no. 740955.250) according to vendor’s manual.
The library preparation was performed according to the manufacturer’s protocol using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD from Lexogen®.
Input mount was 100 ng of total RNA. Bead purified libraries were normalized and finally sequenced on the NextSeq2000 system (Illumina Inc. San Diego, USA) with a read setup of SR 1x100bp.

value: 100 ng/ml IL-6


title: BaF3_ChimP3V3:gp130Box1/2_stimuliert_2


title: BaF3_ChimP3V3:gp130Box1/2_stimuliert_1


title: BaF3_ChimP3V3:gp130Box1/2_stimuliert_3


title: Adipo-4H


title: Participant18_V1D3


title: WT_D7_Xist_CHART rep2


title: Participant12_V1D3

description: we do not have processed data files


title: 3rG4_cl6_D7_Xist_CHART rep1


title: BaF3_ChimP3V3:gp130Box1/2_NC3

value: Medium


title: Adipo-D0


title: Participant12_V3D3


title: BaF3_ChimP3V3:gp130Box1/2_NC4


title: Adipo-12H


title: Adipo-2H


title: BaF3_ChimP3V3:gp130Box1/2_NC1


title: Participant12_V3D0


title: WT_D7_Xist_CHART rep1


title: BaF3_ChimP3V3:gp130Box1/2_NC2


title: Adipo-0H


title: BaF3-gp130:IL-6R wt_stimuliert_4


title: 3rG4_cl5_D7_Xist_CHART rep2


title: Participant12_V2D3


title: 7068-04-001-071

city: Zeist

first: Lars

last: Verschuren

address: Utrechtseweg 48

department: Microbiology and Systems Biology

country: Netherlands

institute: TNO

data_processing:
Quality filtering and adapter-trimming of the Illumina NovaSeq6000 fastq files was performed by TRIMMOMATIC software
Trimmed Fastq files were merged (in case of Paired-end reads) and aligned to the reference genome using the STAR 2.5 algorithm with default settings (https://github.com/alexdobin/STAR).
Based on the mapped read locations and the gene annotation, Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count.files.
Assembly: Mus_musculus.GRCm38.gencode.vM19
Supplementary files format and content: The count files contain the # reads mapped per gene (not normalised per sample). These counts serve as input for the statistical analysis using DEseq2 package.

source_name: liver (FFPE = Formalin Fixed Paraffin Embedded)

extract_protocol:
Next Generation Sequencing (NGS) was performed on archived formalin-fixed paraffin-embedded (FFPE) human liver biopsies (using 10 μm tissue sections) from the translation cohort. Total RNA was extracted using the Ambion RNAqueous total RNA isolation kit (Thermo Fisher Scientific, Inc, Waltman, MA, kit #AM1912). The RNA concentration was determined using a Nanodrop 1000 spectrophotometer (Isogen Life Science, De Meern, Netherlands), and RNA quality was evaluated using the 2100 Bioanalyzer (Agilent Technologies, Amstelveen, Netherlands). Out of the 74 samples of human formalin-fixed paraffin-embedded (FFPE) liver, a subset of 67 samples passed Quality Control (QC) and was selected for RNA sequencing. The QC process involved evaluation of the total RNA concentration and DV200 values (using a Fragment Analyser), which represent the proportion of RNA fragments exceeding 200 nucleotides as determined from the outcomes of electropherograms.
From the selected samples, ribosomal RNA (rRNA) was depleted from total RNA (rRNA depletion kit NEB# E6310, Biolabs), the total RNA was processed into tagged random sequence libraries (NEBNext Ultra II Directional RNA Library Prep Kit, NEB #E7760S/L for Illumina, Biolabs) and sample quality was checked for proper size distribution (300-500 bp peak, Fragment Analyzer). The mixed (multiplex) sample libraries were sequenced on an Illumina NovaSeq6000 sequencer with a paired-read 150-cycle sequencing protocol at GenomeScan BV (Leiden, the Netherlands), resulting in at least 40 million reads per sample.
Clustering and DNA sequencing using the NovaSeq6000 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used yielding paired end reads (2x 150bp). NovaSeq control software NCS v1.6 was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.

tag: fibrosisscore


title: Participant18_V1D0


title: 7068-04-001-070

value: liver (FFPE = Formalin Fixed Paraffin Embedded)


title: Participant11_V2D3


title: BaF3-gp130:IL-6R wt_stimuliert_3

tag: cell line


title: 7068-04-001-072


title: 7068-04-001-068


title: Participant11_V3D3

tag: dose


title: BaF3-gp130:IL-6R wt_stimuliert_2


title: BaF3-gp130:IL-6R wt_stimuliert_1


title: 7068-04-001-069


title: Participant11_V2D0

tag: experimental sequence


title: BaF3-gp130:IL-6R wt_NC3


title: 7068-04-001-065


title: BaF3-gp130:IL-6R wt_NC4


title: 3rG4_cl5_D7_Xist_CHART rep1

value: Day 7 differentiated mouse embryonic stem cells


title: Participant11_V1D0

value: Placebo

tag: study site


title: 7068-04-001-067


title: Participant11_V1D3

value: peripheral whole blood

tag: age (yrs)


title: BaF3-gp130:IL-6R wt_NC1


title: shHmbox1_IRI_2

city: shanghai

first: Yujiao

last: Zhu

address: Nanchen Road 381

institute: Shanghai University

data_processing:
The transcriptome sequencing was performed on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the mm14 genome using HISAT2.
FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
DESeq2 was used for gene expression analysis.

source_name: heart

growth_protocol: Male C57BL/6J mice of eight-to-ten weeks old were purchased from Charles River (Beijing, China) and maintained in SPF laboratory animal facility.  Mice were fed a standard diet for 1 week of adaptive feeding.

extract_protocol:
Total RNAs were extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer's instructions.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: Pre-treatment with sh-Hmbox1 AAV9 or control AAV9 vectors via tail vein 1 week before I/R or sham surgery

value: heart


title: Participant12_V2D0

tag: plasma etg_(ng/ml)


title: 7068-04-001-064


title: WT_D7_Xist_CHART rep2 input

value: WT


title: 7068-04-001-063


title: Con_IRI_3


title: shHmbox1_IRI_1


title: Con_IRI_2


title: Participant9_V2D3

value: PBMC

value: MediumDose

tag: plasma ets_(ng/ml)


title: Participant11_V3D0


title: Participant9_V3D0


title: cecum, OA08, female

city: Bethesda

first: Octavio

last: Mondragon Palomino

address: 4 MEMORIAL DR

institute: National Institutes of Health

data_processing:
RNA-seq results were processed using the R package DESeq2 to obtain variance stabilized count reads, fold changes relative to specific condition, and statistical P-value. Analysis of the OA isolates focused on differentially expressed genes (DEGs), defined as the genes with an absolute fold change relative to specific condition >1 and an adjusted P value < 0.05.
Assembly: mm10
Supplementary files format and content: RawCountFile_rsemgenes.txt tab-delimited text file with raw counts for all samples
Supplementary files format and content: normalized_counts.txt tab-delimited text file with normalized counts for all samples

source_name: cecum

extract_protocol:
Once we verified that the negative control was germ-free, we euthanized the mice and collected cecal tissue for total RNA extraction. Using a biopsy puncher with a diameter of 8mm we collected circular tissue pieces from the cecum of mice and preserved them in DNA/RNA Shield (Zymo Research Corporation, Irvine CA) at -80C. Total RNA was extracted using a kit (Quick-RNA MiniPrep Plus, Zymo Research Corporation). Because the tissue samples were not homogenized, tissues were treated overnight with 2X proteinase K from the kit and constant tumble-mixing until tissues were dissolved. The tissue digest was taken through the protocol provided by the manufacturer, including a step for the enzymatic degradation of DNA. To validate the extraction process, the nucleic acid concentration in the eluates was measured in a spectrophotometer.
Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus

value: cecum

tag: Sex

value: female

value: monocolonized with OA8


title: Participant9_V2D0

tag: tissue

value: Male

value: Not Detected


title: Con_IRI_1


title: 7068-04-001-060


title: Participant9_V1D3

value: HighDose


title: BaF3-gp130:IL-6R wt_NC2


title: cecum, OA08, male, biol rep 2

value: male


title: shHmbox1_IRI_3


title: Participant8_V1D0


title: 7068-04-001-058


title: Participant9_V3D3


title: 7068-04-001-062


title: cecum, OA08, male, biol rep 1


title: 7068-04-001-057


title: Con_Sham_2


title: cecum, OA02, male, biol rep 2

value: monocolonized with OA2


title: Participant8_V3D0


title: Con_Sham_1


title: shHmbox1_Sham_3


title: cecum, OA06, female

value: monocolonized with OA6


title: shHmbox1_Sham_2


title: 7068-04-001-059

value: liver (FFPE = Formalin Fixed Paraffin Embedded)


title: Participant9_V1D0


title: cecum, OA06, male, biol rep 2


title: shHmbox1_Sham_1


title: cecum, OA06, male, biol rep 1


title: Con_Sham_3


title: Participant8_V3D3


title: JHU083, CD45+ immune cells, mouse 752

first: Alex

middle: Jea-Eun

last: Lee

state: MD

address: 1650 Orleans Street

institute: Johns Hopkins University

description: 10X Genomics

data_processing:
Demultiplexing, barcode processing, and gene counting and aggregation were made using the Cell Ranger software v7.0.0
Assembly: mm10
Supplementary files format and content: HDF5 files from the cellranger count pipeline, each containing the count data for each sample

source_name: Sub-cutaneous tumor

growth_protocol: B6CaP cells were injected subcutaneously into the flank region of each mouse.

extract_protocol:
RNA was extracted from sorted cells (Live CD45+ or CD45-) by first using the NextGEM protocol on 10X Chromium X, following manufacturer's instructions.
Library construction was performed according to manufacturer's instructions (single cell 3' v3.1 protocol, 10X Genomics)

treatment_protocol: Each mouse was treated with either PBS (control) or JHU083 by oral gavage.

value: Sub-cutaneous tumor

value: CD45+ sorted cells

value: Male C57BL/6J

value: JHU083 oral gavage


title: 7068-04-001-061


title: Participant7_V2D3

value: peripheral whole blood

value: Placebo

value: Female


title: Participant7_V2D0

value: PBMC


title: 7068-04-001-052


title: JHU083, CD45+ immune cells, mouse 745

description: 10X Genomics


title: cecum, OA02, female

value: cecum

value: female


title: 7068-04-001-056


title: 7068-04-001-055


title: 7068-04-001-051


title: cecum, GERM FREE, male, biol rep 1

value: germ free mouse


title: cecum, OA02, male, biol rep 1


title: Participant8_V2D0

value: MediumDose

value: Male

value: Not Detected


title: Participant8_V2D3


title: JHU083, CD45- tumor cells, mouse 752

description: 10X Genomics

value: CD45- sorted cells


title: Participant6_V3D3


title: cecum, GERM FREE, female


title: 7068-04-001-053


title: 7068-04-001-049


title: cecum, GERM FREE, male, biol rep 2

value: male


title: JHU083, CD45+ immune cells, mouse 725

description: 10X Genomics


title: 7068-04-001-054

value: liver (FFPE = Formalin Fixed Paraffin Embedded)


title: JHU083, CD45- tumor cells, mouse 725

description: 10X Genomics

value: Sub-cutaneous tumor


title: KT_3

city: Pamplona

first: Elizabeth

last: Guruceaga

address: Pio XII 55

country: Spain

institute: CIMA

data_processing:
The quality of the samples was verified using FastQC v0.11.8 software.
FASTQ files were mapped to GRCm39 human assembly using STAR v2.7.9a with default parameters.
featureCounts v1.6.0 software and Gencode vM31 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions
Obtained gene counts were normalized using edgeR and voom function of limma
Supplementary files format and content: GRCm39
Supplementary files format and content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: Lung

growth_protocol: Murine LUAD cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C; Trametinib resistant cells were maintained in DMEM with trametinib 500nM

extract_protocol:
RNA was harvested using TRIzol  (Thermo Fisher Scientific). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: cells were treated with trametinib 72h 100nM or with DMSO (Control cells).

value: Lung

value: KLA

value: Lung Adenocarcinoma

value: KRAS-mutant

value: Trametinib 100nM 72h


title: 7068-04-001-048


title: 7068-04-001-050


title: JHU083, CD45- tumor cells, mouse 745

description: 10X Genomics

value: Male C57BL/6J

value: JHU083 oral gavage


title: KSC_3


title: Participant6_V3D0

value: peripheral whole blood

value: PBMC

value: Female


title: KT_2


title: Participant6_V2D3

value: HighDose


title: Participant6_V2D0


title: Control, CD45+ immune cells, mouse 784

description: 10X Genomics

value: CD45+ sorted cells

value: PBS oral gavage


title: Control, CD45+ immune cells, mouse 780

description: 10X Genomics


title: 7068-04-001-047


title: Participant6_V1D3

value: Placebo

value: Not Detected


title: Control, CD45- tumor cells, mouse 780

description: 10X Genomics

value: CD45- sorted cells


title: Participant5_V2D0

value: Male


title: Participant6_V1D0


title: KT_1

value: Lung


title: 7068-04-001-046

value: liver (FFPE = Formalin Fixed Paraffin Embedded)


title: CTR_2

value: Lung Adenocarcinoma


title: KSC_1

value: KLA

value: KRAS-mutant


title: Control, CD45+ immune cells, mouse 749

description: 10X Genomics

value: Sub-cutaneous tumor

value: Male C57BL/6J


title: Control, CD45- tumor cells, mouse 749

description: 10X Genomics


title: CTR_1

value: Trametinib 100nM 72h


title: Participant5_V1D0

value: peripheral whole blood

value: PBMC

value: MediumDose


title: 7068-04-001-045


title: 7068-04-001-044


title: JHU083, TAMs, mouse 964

data_processing:
rsem-1.3.0 was used for alignment to the mm39 genome and for the generation of gene expression levels.
The following options were used in the rsem-calculate-expression module: --star --calc-ci --star-output-genome-bam --forward-prob 0.5
Differential expression analysis and statistical testing was performed with DESeq2.
Assembly: mm39
Supplementary files format and content: tab-delimited text files from the rsem pipeline, including counts, TPM, and FPKM for each sample
Supplementary files format and content: DESeq2 results comparing JHU083-treated TAMs versus control TAMs

extract_protocol:
Total RNA was extracted from sorted tumor associated macrophages (Live CD45+CD3-Ly6G-CD11b+F4/80+) with Trizol (Thermofisher) based on manufacturer's protocol.
RNA was converted to cDNA with the Ovation RNA-seq System v2.0 kit and library construction was performed with the Truseq Nano kit (Illumina).

value: Tumor associated macrophages

value: JHU083 oral gavage


title: 7068-04-001-042


title: CTR_3


title: Participant4_V3D3

value: Placebo


title: Participant5_V1D3

value: Not Detected


title: JHU083, TAMs, mouse 963


title: CT_2


title: KSC_2


title: CT_3


title: 7068-04-001-041


title: CT_1


title: 7068-04-001-043


title: JHU083, TAMs, mouse 958


title: Participant4_V3D0


title: Control, CD45- tumor cells, mouse 784

description: 10X Genomics

value: CD45- sorted cells

value: PBS oral gavage


title: Participant5_V2D3

value: Male

value: BLQ


title: JHU083, TAMs, mouse 957


title: JHU083, TAMs, mouse 956


title: 7068-04-001-039

value: liver (FFPE = Formalin Fixed Paraffin Embedded)


title: 7068-04-001-037


title: 7068-04-001-040


title: Participant4_V1D3

value: HighDose


title: Participant4_V1D0


title: CSC_3

value: Lung

value: Lung Adenocarcinoma

value: KRAS-mutant


title: JHU083, TAMs, mouse 955

value: Sub-cutaneous tumor

value: Male C57BL/6J


title: Control, TAMs, mouse 962


title: CSC_2


title: 7068-04-001-038


title: CSC_1


title: Participant3_V3D0

value: peripheral whole blood

value: PBMC


title: sample.24_Colon_bulk_KO_aPD1_5

city: St. Louis

first: Marco

last: Colonna

state: MO

address: 660 S. Euclid Ave

department: Immunology&Pathology

institute: Washington University in St. Louis

data_processing:
3' scRNAseq data was processed using the cellranger count pipeline (CellRanger version 7.1.0, 10X Genomics) with default settings.
RNA-seq reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 4.0.3-8 software. tab-delimited file containing the raw reads count matrix
Assembly: GRCm38
Supplementary files format and content: filtered_feature_bc_matrix folder contents produced by the CellRanger pipelines, containing three files per sample: barcodes.tsv.gz,  features.tsv.gz and matrix.mtx.gz. For Bulk RNAseq all.genes_counts.tsv
Supplementary files format and content: all.genes_counts.tsv is a tab-delimited file containing the raw reads count matrix

source_name: Colon lamina propria

extract_protocol:
For scRNAseq: Using the Chromium Single Cell 3′ Reagent Kit v2 or v3User Guide, single cell suspensions were partitioned into nanoliter droplets called Gel-bead-in-Emulsions (GEMs) to achieve single cell resolution. The cDNA generated within each individual GEM is tagged with a common 16nt 10x barcode and a 12nt unique molecular barcode during the RT reaction. Purified cDNA was amplified for 11 cycles before being purified using SPRIselect beads. Samples were then run on a Agilent Bioanalyzer to determine cDNA concentration. 10uL of purified cDNA was used to generate the Illumina library for sequencing. For Bulk RNA seq: total tissue RNA was extracted using RNA easy mini kit. Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation.
For scRNAseq: For sample preparation on the 10x Genomics platform, the Chromium Single Cell 3′ GEM, Library & Gel Bead Kit v3 16 rxns (PN-1000075), Chromium Chip B Single Cell Kit, 48 rxns (PN-1000073) and Chromium i7 Multiplex Kit (PN-120262) were used. The single cell libraries were then sequenced on the Illumina NovaSeq 6000 S4 200 cycle flow cell generating 28x98 reads. A median sequencing depth of 50,000 reads/cell was targeted for each sample. For bulk RNAseq: Library preparation was performed with 5 to 10ug of total RNA with a Bioanalyzer RIN score greater than 8.0. Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags.

value: Colon lamina propria

value: total cells

tag: strain background


title: 7068-04-001-033


title: Participant3_V2D3

tag: cell type

value: MediumDose


title: Control, TAMs, mouse 961

value: Tumor associated macrophages


title: 7068-04-001-035


title: Control, TAMs, mouse 959


title: sample.23_Colon_bulk_KO_aPD1_4


title: 7068-04-001-032


title: sample.22_Colon_bulk_KO_aPD1_3


title: Control, TAMs, mouse 954


title: 7068-04-001-031


title: Participant3_V1D0

value: Placebo

tag: gender

value: Not Detected


title: 7068-04-001-030


title: Participant2_V3D3

value: Male


title: sample.21_Colon_bulk_KO_aPD1_2

tag: genotype


title: Participant3_V3D3


title: 7068-04-001-029


title: Participant2_V3D0


title: sample.18_Colon_bulk_WT_aPD1_6

value: WT

tag: treatment


title: Control, TAMs, mouse 953

value: PBS oral gavage


title: Control, TAMs, mouse 951


title: sample.17_Colon_bulk_WT_aPD1_5


title: 7068-04-001-028

value: liver (FFPE = Formalin Fixed Paraffin Embedded)


title: Participant2_V2D0

value: HighDose


title: sample.16_Colon_bulk_WT_aPD1_4


title: 7068-04-001-027


title: Participant2_V2D3


title: Sham,0,39

city: Atlanta

first: Levi

middle: B.

last: Wood

state: GA

address: 315 Ferst Dr NW Rm 3303

institute: Georgia Institute of Technology

data_processing:
Alignment and calculation of count matrix was performed by Admera Health using mm10 plus 3xTg transgenes APP, MAPT, PSEN1.
Assembly: mm10
Supplementary files format and content: Comma separated values of count matrix

source_name: Somatomotor cortex, left hemisphere

extract_protocol: RNA was isolated from mouse somatomotor cortices using Qiagen RNeasy kit (217804; Qiagen; Hilden, Germany) according to the manufacturer’s protocols.

value: Somatomotor cortex, left hemisphere

value: Female

tag: injury

value: Sham

tag: time point_after_last_injury

tag: time point_from_start


title: 4xCHI,24,40


title: Participant3_V2D0


title: 7068-04-001-026

tag: fibrosisscore


title: 3xCHI,24,38


title: Participant1_V3D3

tag: dose


title: sample.15_Colon_bulk_WT_aPD1_3


title: sample.12_Colon_bulk_KO_5


title: 7068-04-001-025


title: Participant1_V3D0

tag: experimental sequence


title: 3xCHI,24,37


title: 7068-04-001-024


title: sample.10_Colon_bulk_KO_4


title: 1xCHI,4,36


title: Participant17_V1D3

tag: study site


title: sample.9_Colon_bulk_KO_3


title: sample.6_Colon_bulk_WT_6


title: 7068-04-001-022


title: 5xCHI,24,34


title: Sham,0,35


title: Participant8_V1D3

tag: age (yrs)


title: sample.5_Colon_bulk_WT_5


title: Participant3_V1D3

tag: plasma etg_(ng/ml)


title: 7068-04-001-021


title: 5xCHI,24,33


title: 7068-04-001-020


title: 5xCHI,4,32


title: C. carpio, diploid, female, replicate_4

city: Brno

first: Andrea

middle: Vetešníková

last: Šimková

address: Kamenice 5

department: Department of Botany and Zoology

country: Czech Republic

institute: Masaryk University

data_processing:
A quality check of raw paired-end fastq reads was carried out by FastQC and their origin was categorized using BioBloomTools v2.3.4. The Illumina adapters clipping and quality trimming of raw fastq reads were performed using Trimmomatic v0.39 with settings CROP:250 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:5 MINLEN:35. Trimmed RNA-Seq reads were mapped to the reference genome using STAR v2.7.3a as a splice-aware short read aligner and default parameters except for --outFilterMismatchNoverLmax 0.1 and --twopassMode Basic. Quality control after alignment concerning the number and percentage of uniquely- and multi-mapped reads, rRNA contamination, mapped regions, read coverage distribution, strand specificity, gene biotypes, and PCR duplication was performed using several tools – namely, RSeQC v4.0.0, Picard toolkit v2.25.6, and Qualimap v.2.2.2. All statistics were processed by MultiQC v1.10.1.
The genomic sequences of all collected samples were aligned to the reference genome utilizing the Burrows-Wheeler Aligner (BWA) software. Post alignment and germline variants were called using Strelka2 variant calling software, generating variant calls in VCF format which were further filtered to retain only high-confidence variants. These variants were then annotated using the reference annotation in GTF file. Subsequent data processing was carried out in R, where the variant tables were further refined and merged with sample information. A series of filtering steps were performed to ensure only variants with sufficient coverage and sample counts were retained for analysis. The filtered variant table was then reorganized and formatted for subsequent comparative analyses. Variants located on sex chromosomes were excluded for certain analyses to ensure accurate cross-species comparisons. The data were then restructured to compare SNP identity across species, generating similarity matrices and Venn diagrams to visualize the overlap of SNPs by species and ploidy levels.
The differential gene expression was calculated on the basis of the gene counts produced using featureCounts from the Subread package v2.0 and further analysed by Bioconductor package DESeq2 v1.34.0. Data generated by DESeq2 with independent filtering were selected for differential gene expression analysis to avoid potential false positive results. Differences in gene expression were considered significant on the basis of a cut-off of the adjusted p-value ≤ 0.05. GO term enrichment was analysed using David to retrieve Gene Ontology terms in the Biological process, Cellular Component and Molecular function categories, as well as KEGG pathways. Graphical representations of the GO enrichment were realized using R and Revigo. Reproduction-associated candidate genes were retrieved using the BlastKoala tool of KEGG, the BioMart tool of Ensembl, and published studies. GO terms enrichment was tested using Fisher’s exact test (α = 0.05) with false discovery rate (FDR) correction of the p-value. To interpret the biological functions of the DEGs, their mapping to the Gene Ontology (GO) and KEGG databases was performed to analyse pathway enrichment. In each of six fish groups associated with sexual reproduction and asexual males, significantly differently-expressed genes (DEGs) compared to the triploid asexual females of C. gibelio were selected on the basis of the following criteria: Basemean > 10, and a padj value < 0.05,. For KEGG pathway analysis, no filtering based on log2 fold change was applied. Gene functions were investigated using the biological databases Uniprot, KEGG, Zfin and GeneCards. PCA was performed using the DESeq2 R package. For PCA based on reproduction-associated genes, a set of 208 reproduction genes was selected using the BioMart tool of Ensembl.
Assembly: Carassius auratus genome (ASM336829v1) with Ensembl annotation (release 104)
Supplementary files format and content: tab-delimited text file includes raw counts for all Samples

organism: Cyprinus carpio

source_name: gonadal

growth_protocol: Asexual and sexual C. gibelio were obtained from artificial breeding. Asexual females were obtained by induced embryogenesis using sperm of C. carpio. The sexual specimens were obtained from the interbreeding of sexual specimens. The fish were reared in aquarium conditions until the age of four years and subsequently their gonadal tissues were sampled (the age of the examined fish corresponded to 4+). Cyprinus carpio and Carassius auratus were obtained from external breeding facilities. Four or five biological samples per fish group from a total of 8 fish groups were analysed (females and males of C. gibelio resulting from sexual reproduction, females and temperature-induced males of C. gibelio resulting from gynogenesis, females and males of sexual C. auratus, and females and males of sexual C. carpio).

extract_protocol:
Total RNA was isolated from the gonad tissue of each fish specimen. For extraction, PureLink® RNA Mini Kit (Ambion) with Trizol reagent (Thermo Fisher Scientific) and on-column PureLink DNase treatment were used according to the manufacturer´s protocol. Reagent and buffer volumes were adjusted according to the weight of tissue entering the isolation process (30 mg on average). The final elution was performed using 100 µl of RNAse-free water in the first step and the primal eluate in the second step. The yield and concentration of RNA isolates were checked using a QubitTM 4 fluorometer (Invitrogen by Thermo Fisher Scientific) and Qubit RNA HS Assay Kit (Thermo Fisher Scientific). The quality and integrity of RNA were analysed using RNA 6000 Nano Kit on a 2100 Bioanalyser instrument (Agilent Technologies). All RNA isolates were normalized by dilution at a uniform concentration of 20 ng/µl with RNase-free water. They served as templates for DNA library preparation in twice the reaction volume recommended by the manufacturer.
All samples (RNA integrity number – RIN > 7) were used for DNA library preparation. 500ng of total RNA was used for mRNA enrichment using the Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). Subsequently, NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®, and NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 2, New England Biolabs) were used for library preparation, with 11 PCR cycles utilized for PCR enrichment. RNA fragmentation (13 minutes at 94°C) and the size selection conditions (a bead volume of 30 µl and 15 µl for the first and second bead selections, respectively) were further modified in the protocol. The quantification of DNA libraries was performed on a QubitTM 4 fluorometer (Invitrogen by Thermo Fisher Scientific) using Qubit dsDNA HS Assay Kit, and quality and size control were performed on a 2100 Bioanalyser with DNA 1000 Kit (Agilent Technologies). Finally, amplicons were pooled in equimolar amounts. The final concentration of each library in the pool was 10 nM in the pool. Subsequently, NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® and NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 2, New England Biolabs) together with spike-in RNA were used for cDNA library preparation from total RNA. The quality of prepared cDNA libraries was evaluated using a Qubit fluorometer (Thermo Fisher). The quality of cDNA libraries was visualized by a 2100 Bioanalyser (Agilent), and the libraries were were finally sequenced by Macrogen Korea on Illumina HiSeq X (one lane) in a paired-end configuration producing 150 bp long reads.

treatment_protocol: Gonadal tissues of each fish specimen were individually submerged in Ambion RNAlater stabilization solution (Thermo Fisher Scientific). Tubes with tissues were stored at -80ºC until the isolation of total RNA.

value: gonadal

tag: ploidy

value: diploid

value: female


title: sample.3_Colon_bulk_WT_3

value: Colon lamina propria


title: C. carpio, diploid, male, replicate_4

tag: Sex

value: male


title: sample.4_Colon_bulk_WT_4

tag: tissue

value: total cells


title: 5xCHI,0.5,31


title: C. carpio, diploid, female, replicate_3


title: 7068-04-001-017


title: pten-l-3

city: Zhengzhou

first: Pan

middle: Zhen

last: Zhen

state: Henan

address: No. 1, Jianshe East Road, Erqi District

institute: First Affiliated Hospital of Zhengzhou University

data_processing:
Quality control and mapping
Gene-level quantification, analysis of differentially expressed genes (DEGs), cluster analysis, GO and KEGG enrichment
Transcript-level quantification, analysis of differentially expressed transcript (DEGs), cluster analysis, GO and KEGG enrichment
Gene structure extension and novel transcripts identification
Alternatively splicing analysis and SNP-INDEL calling
Assembly: mm10
Supplementary files format and content: Tab-delimited text files includes raw counts for each sample
Supplementary files format and content: Tab-delimited text files includes RPKM values for each sample

source_name: breast

growth_protocol: These cells were cultured in DMEM (Gibco, Carlsbad, CA, USA) containing 10% FBS, 100 IU/mL penicillin, and 100 mg/mL streptomycin at 37℃ with 5% CO2.

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. RNA  purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo  Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent  Technologies, Santa Clara, CA, USA)
Then the libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

treatment_protocol: After treating the cells separately with PBS and PTEN-L for 2 hours, collect the cells.

value: breast

tag: cell line

value: mouse mammary carcinoma cell line

value: PTEN-L


title: 7068-04-001-019


title: C. carpio, diploid, male, replicate_3


title: 3xCHI,4,30


title: pten-l-2

tag: cell type


title: 7068-04-001-015


title: 2xCHI,24,29


title: 7068-04-001-014


title: 7068-04-001-023


title: C. carpio, diploid, male, replicate_2


title: pten-l-1


title: 1xCHI,24,28


title: ctrl-3

value: PBS


title: C. carpio, diploid, male, replicate_1


title: 7068-04-001-013


title: 7068-04-001-012


title: 1xCHI,0.5,27


title: C. carpio, diploid, female, replicate_1


title: 1xCHI,24,26


title: ctrl-1


title: 4xCHI,24,25


title: RV free wall, PAB-operated, P21, ATAC-seq, rep3

city: Shanghai

first: Yuqing

last: Hu

address: 1678 Dongfang Road, Pudong New District, Shanghai

institute: Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected.We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
GATK2 (v3.7) software was used to perform SNP calling. Raw vcf files were filtered with GATK standard filter method and other parameters (cluster:3; WindowSize:35; QD < 2.0 o; FS > 30.0; DP < 10 and SnpEff software was used to annotation for the Variablesite.
Differential expression analysis of two conditions/groups (three biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Alternative Splicing is an important mechanism for regulate the expression of genes and the variable of protein. rMATS(3.2.5) software was used to analysis the AS event.
PPI analysis of differentially expressed genes was based on the STRING database, which known and predicted Protein-Protein Interactions.
WGCNA (Weighted correlation network analysis) was used to describe the gene association modes among different samples.
For ATAC-seq, illumina Casava2.19 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.19.11).
These reads were aligned to a reference genome using BWA, with standard parameters. These reads were then filtered for high quality (MAPQ≥ 13), non mitochondrial chromosome, and properly paired reads (longer than 18 nt).
All peak calling was performed with macs2 using ‘macs2 callpeak --nomodel --keepdup all --call-summits’.
Assembly: Rnor_6.0.97
Supplementary files format and content: FPKM

organism: Rattus norvegicus

source_name: RV free wall myocardium

extract_protocol:
Myocardium of RV free wall was rapidly removed from executed rat and flash frozen in liquid nitrogen, RNA was harvested using Trizol reagent. Nuclei was extracted from samples, and the nuclei pellet was resuspended in the Tn5 transposase reaction mix. The transposition reaction was incubated at 37°C for 30 min.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Equimolar Adapter1 and Adatper 2 were added after transposition, PCR was then performed to amplify the library. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit.

value: RV free wall myocardium

tag: strain

value: Sprague-Dawley

tag: developmental stage

value: postnatal day 21

value: WT

value: pressure overload(PAB)


title: 7068-04-001-010

value: liver (FFPE = Formalin Fixed Paraffin Embedded)


title: 7068-04-001-009


title: 220415_lib_3

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

data_processing:
Raw data (cellranger bam files) has been deposited under European Genome-Phenome Archive (EGA) accession number EGAS0000xxxxxx.
Raw data were analyzed using Cell Ranger Single-cell software v6.0.0 against hg38 genome.
The single-cell RNA-seq data were processed and analyzed  by Seurat package v4.0 (2) using R.4.02.
Assembly: hg38
Supplementary files format and content: HDF5 cellranger output file per sample

source_name: Blood and/or bone marrow

extract_protocol:
Stored frozen cells were thawed and processed according to the Chromium Next GEM Single Cell 5 procedure from 10XGenomics.
Chromium Next GEM Single Cell 5'Reagent Kits v2 with feature barcoding (10X Genomics)

value: Blood and/or bone marrow


title: C. carpio, diploid, female, replicate_2

value: gonadal


title: RV free wall, PAB-operated, P21, ATAC-seq, rep2

tag: genotype

tag: treatment


title: 220415_lib_1


title: 3xCHI,24,23

value: Somatomotor cortex, left hemisphere

value: Female

tag: injury

tag: time point_after_last_injury


title: 220415_lib_2


title: RV free wall, PAB-operated, P21, ATAC-seq, rep1


title: 3xCHI,0.5,22

tag: time point_from_start


title: 7068-04-001-008

tag: fibrosisscore


title: CDKN2B-AS1 OE3

city: Sendai

first: Kota

last: Sato

state: Miyagi

address: 1-1, Seiryo-machi, Aoba-ku

department: Ophthalmology

institute: Tohoku University

data_processing:
The obtained reads were mapped to the mouse GRCh38.p13 (hg38) genome with STAR software (version 2.7.9). Reads of annotated genes were counted using featureCounts software (version 2.0.1). FPKM values were calculated from mapped reads by normalizing to total counts and the transcript.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

extract_protocol:
Total RNA were  extracted with RNeasy Micro kit (74004, Qiagen).
RNA-seq libraries were synthesized with the SMART-seq HT Kit (634455, Clontech). RNA-seq libraries were sequenced using paired end reads (150 nt for read 1 and  read 2) on a DNBSEQ-G400RS (MGI Tech, Shenzhen, China).

value: neuroblastoma

value: CDKN2B-AS1 overexpression


title: RV free wall, sham-operated, P21, ATAC-seq, rep3

value: sham-operated


title: 7068-04-001-007


title: RV free wall, sham-operated, P21, ATAC-seq, rep2


title: ctrl-2

value: breast


title: 7068-04-001-006


title: RV free wall, sham-operated, P21, ATAC-seq, rep1


title: CDKN2B-AS1 OE2


title: CDKN2B-AS1 OE1


title: 7068-04-001-011


title: 7068-04-001-005


title: RV free wall, PAB-operated, P21, RNA-seq, rep3


title: 4xCHI,24,24


title: 2xCHI,24,19


title: RV free wall, PAB-operated, P21, RNA-seq, rep2


title: stuffer 2

value: control vector infection


title: RV free wall, PAB-operated, P21, RNA-seq, rep1


title: 7068-04-001-002


title: stuffer 1


title: 7068-04-001-003


title: 1xCHI,4,16


title: PC9_Erlo_DTEC_3

city: Toulouse

first: Juan Pablo

last: Cerapio

address: Av 2 Hubert Curien

institute: CRCT

data_processing:
bcl2 files conversion to FASTQ format using bcl2fastq algorithm
align to the GRCh38 reference transcriptome using bowtie2
Preprocessing, normalization, QC, and downstream analysis were performed using Deseq2 in R enviroment
The processed (sample x gene) matrix counts are provided.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw counts for every gene and every sample

source_name: lung adenocarcinoma

growth_protocol: The human EGFR-mutant NSCLC PC9, HCC4006, H3255 and HCC827 cell lines were subcloned and amplified in drug-free RPMI (Roswell Park Memorial Institute) 1640 medium containing 10% fetal bovine serum (FBS) and were maintained at 37°C in a humidified chamber containing 5% CO2. Cell lines were authenticated and tested for mycoplasma contamination within the experimental time frame.

extract_protocol:
RNA extraction was performed using AllPrep DNA/RNA Mini kit (Qiagen, #80204) according to the manufacturer’s protocol. RNA quality was assessed using Fragment Analyzer (Agilent technologies) and the RQN values were provided to confirm the integrity of total RNA. RNA concentration was determined by fluorescent method using Quant-iT™ RNA Assay Kit, Broad Range (ThermoFisher Scientific).
RNA samples were processed with Illumina TruSeq® Stranded mRNA Library Preparation Kit following the manufacturer’s protocol. Library size and quality were confirmed on Fragment analyzer (Agilent Technologies). KAPA quantification kit for Illumina platforms (KAPA Biosystems, Roche) was used to quantify the library by qPCR. Indexed libraries were pooled and sequenced on an Illumina NextSeq 550 (2x75 bp paired-end reads).

treatment_protocol: EGFR-mutant NSCLC PC9, HCC4006, H3255 and HCC827 cell lines were subcloned and amplified in drug-free RPMI (Roswell Park Memorial Institute) 1640 medium containing 10% fetal bovine serum (FBS) and were maintained at 37°C in a humidified chamber containing 5% CO2. PC9, HCC4006 and H3255 subclones were treated with DMSO (control) or with erlotinib at 1 µM for 24h, until drug-tolerance (7-to-21 days) or until development of fully resistant proliferative cells (RPC, only for PC9 and HCC4006 cells). RPC were isolated and amplified from individual early-emerging colonies, which were cultured and passaged for more than three months in the presence of the drug. HCC827 were treated with DMSO (control) or with osimertinib at 1 µM until drug-tolerance (11 days).

value: lung adenocarcinoma

value: epithelial cell

tag: subcloned

value: yes

value: erlotinib 1 uM, 21 days


title: RV free wall, sham-operated, P21, RNA-seq, rep2

value: RV free wall myocardium

value: Sprague-Dawley

value: postnatal day 21


title: 7068-04-001-001

value: liver (FFPE = Formalin Fixed Paraffin Embedded)


title: PC9_Erlo_DTEC_2


title: Sham,0,20

value: Sham


title: Tranduced with RFP sample 3

city: New York

first: David

last: Requena

state: NY

address: 1230 York Avenue

institute: Rockefeller University

data_processing:
Quality assessment and trimming were performed using FastQC v0.11.9, MultiQC v1.11 (Ewels et al., 2016) and BBDuk (included in BBMap v38.95).
Reads per transcript were quantified using Salmon (Patro et al., 2017) with the human reference genome hg38 with the EMSEMBL GRCh38.103 gene annotations as template.
Differential gene expression analysis was conducted in R v4.2.0 and RStudio 2022.07.1+554 using DESeq2 v1.36.0, excluding genes corresponding to rRNAs and mt-rRNAs.
Assembly: hg38
Supplementary files format and content: a MS Excel file including raw gene counts for each sample
Supplementary files format and content: a MS Excel text file including Deseq-normalized counts for each sample

source_name: liver

growth_protocol: PHH cells were maintained in Hepatocyte culture medium (Lonza-CC-3199) supplamented with HCM SingleQuot (CC-4182) and Puromycine at 37C with 5% CO2.

extract_protocol:
Total RNA from PHH cells was extracted using the RNeasy Mini Kit (Qiagen). RNA concentration levels were measured in a Nanodrop 2000c (Thermofisher) using the 260/280 ratio. RNA Integrity Values (RIN) were measured in an Agilent BioAnalyzer and TapeStation.
Paired-end 2x150nt RNA-seq libraries were prepared using TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero (Gold) for rRNA and mt-rRNA depletion (Illumina).

treatment_protocol: Cells that were transduced with different constructs expressiing DNAJB1::PRKACA, PRKACA,  ATP1B1::PRKACA, DNAJB1::PRKACA K128H, and RFP. After selection with Puromycine, cells were maintained in HCM media with no treatment.

value: liver

value: Primary human hepatocytes

value: Tranduced with RFP


title: 2xCHI,24,21

value: Somatomotor cortex, left hemisphere

value: Female


title: 1xCHI,4,15


title: RV free wall, sham-operated, P21, RNA-seq, rep1

value: WT

value: sham-operated


title: 1xCHI,0.5,14


title: Tranduced with RFP sample 2


title: INPUT, PI, REP1

city: Paris

first: Claudia

last: Chica

address: 25-28 Rue du Dr Roux

institute: Institut Pasteur

data_processing:
Complete analysis from the raw sequencing data to the differential marking analysis was done following the ePeak approach (cite https://doi.org/10.1093/nargab/lqac041).
Default parameters were used for the filtering, mapping of reads and narrow peak calling.
For H3K4me2, reproducible peaks were determined using the intersection approach, requiring at least 40% length overlap between replicates. For H3K4me3, reproducible peaks were determined using the IDR method. Coverage per replicate and for pooled replicates was calculated using nibs of 10bp and the CPM normalization method.
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: PI

growth_protocol: The human alveolar epithelial cell line A549 (ATCC CCL-185) were cultured in F-12K culture medium (Gibco™ 21127030) supplemented with 10% fetal calf serum (FCS) and 1% L-glutamine and incubated at 37 °C in a humidified atmosphere with 5% CO2. Bacteria (pneumococcus) were diluted in serum-low cell culture medium (0,25% FCS) to get a multiplicity of infection of 20:1 (MOI 20). After 3h of  infection (primary), cells were washed twice with PBS to remove the unattached bacteria, and then either collected for analysis, or cultured in medium with penicillin-streptomycin (10 microg /ml) and gentamicin (200 microg /ml) for later time point (PI).

extract_protocol: ChIP and input samples were treated with IPure Kit (Diagenode, C03010015) followed protocol according to manufacturers’ instructions. ChIP and input DNA were quantified with Qubit 4 fluorometer (ThermoFisher). The libraries were performed with 10 ng each sample.

treatment_protocol: Cells were cross-linked with 1% formaldehyde 8 min at room temperature, followed by quenching with 0,125 M glycine for 5 min. After two washes in PBS, cells were collected by scraping then pelleted and lysed on ice for 5 min in 0.25% Triton X-100, 10 mM Tris-HCl (pH 8), 10 mM EDTA, 0.5 mM EGTA and proteases inhibitors. The soluble fraction was eliminated by centrifugation and chromatin was extracted with 250 mM NaCl, 50 mM Tris-HCl (pH 8), 1 mM EDTA, 0.5 mM EGTA and proteases inhibitors cocktail for 30 min on ice. Chromatin was resuspended in 1% SDS, 10 mM Tris-HCl (pH 8), 1 mM EDTA, 0.5 mM EGTA and proteases inhibitors cocktail, then fragmented by sonication (10 cycles of 30 sec ‘on’ and 30 sec ‘off’) using Bioruptor Pico (Diagenode). Sheared chromatin was cleared by centrifugation, sampled for the shearing efficiency analysis with High Sensitivity DNA kit (Agilent, 5067-4626) using 2100 Bioanalyzer instrument (Agilent). 2 μg of antibodies ChIP-grade (H3K4me2, H3K4me3, H3, Normal Rabbit IgG). 2% of ChIP sample volume was reserved to serve as input. Diluted chromatin was then added to antibody bound DiaMag beads and incubated at 4˚C overnight with gentle rotation. ChIP samples were washed sequentially 5 min with buffer 1 (1% Triton X-100, 0.1% NaDOC, 150 mM NaCl, 10 mM Tris-HCl (pH 8)), buffer 2 (0.5% NP-40, 0.5% Triton X-100, 0.5 NaDOC, 150 mM NaCl, 10 mM Tris-HCl (pH 8)), buffer 3 (0.7% Triton X-100, 0.1% NaDOC, 250 mM NaCl, 10 mM Tris-HCl (pH 8)), buffer 4 (0.5% NP-40, 0.5% NaDOC, 250 mM LiCl, 20 mM Tris-HCl (pH 8), 1 mM EDTA), buffer 5 (0,1% NP-40, 150 mM NaCl, 20 mM Tris-HCl (pH 8), 1 mM EDTA) and buffer 6 (10 mM Tris-HCl (pH 8), 1 mM EDTA).

value: lung carcinoma epithelial cells

tag: chip antibody

tag: infection

value: PI


title: PC9_Erlo_DTEC_1

value: lung adenocarcinoma

value: epithelial cell


title: 1xCHI,0.5,13


title: 7068-04-001-004


title: stuffer 3

value: neuroblastoma

value: control vector infection


title: PC9_Erlo_DTC_3

value: yes

value: erlotinib 1 uM, 7 days


title: 5xCHI,24,12


title: 1xCHI,24,18


title: 1xCHI,24,17


title: INPUT, primary, REP1

source_name: primary

value: primary


title: RV free wall, sham-operated, P21, RNA-seq,  rep3

value: RV free wall myocardium

value: Sprague-Dawley

value: postnatal day 21


title: PC9_Erlo_DTC_2


title: Transduced with PRKACA sample 3

value: liver

value: Primary human hepatocytes

value: Transduced wiht PRKACA


title: PC9_Erlo_DTC_1


title: 5xCHI,24,11

value: Somatomotor cortex, left hemisphere

value: Female


title: Transduced with PRKACA sample 2


title: INPUT, UI, REP1

source_name: UI

value: lung carcinoma epithelial cells

value: UI


title: H3K4me3, PI, REP2

value: ChIP-grade Diagenode C15410003

value: PI


title: 5xCHI,4,10


title: Transduced with PRKACA sample 1


title: H3K4me3, PI, REP1


title: 5xCHI,4,09


title: PC9_Erlo_24h_3

value: lung adenocarcinoma

value: epithelial cell

value: erlotinib 1 uM, 24h


title: Transduced with an inactive DNAJB1::PRKACA sample 3


title: PC9_Erlo_24h_2

value: yes


title: H3K4me3, primary, REP2

value: primary


title: 5xCHI,0.5,08


title: 5xCHI,0.5,07


title: PC9_CT_24h_3

value: DMSO


title: H3K4me3, primary, REP1


title: Transduced with an inactive DNAJB1::PRKACA sample 1


title: Sham,0,06

value: Sham


title: PC9_CT_24h_2


title: 3xCHI,0.5,05


title: PC9_CT_24h_1


title: Transduced with DNAJB1::PRKACA sample 3

value: Transduced with DNAJB1::PRKACA


title: PC9_3_NT1_2


title: Tranduced with RFP sample 1

value: liver

value: Tranduced with RFP


title: 3xCHI,4,03


title: H3K4me2, PI, REP2

value: ChIP-grade Abcam ab32356


title: H3K4me2, PI, REP1


title: H3K4me3, UI, REP2


title: 3xCHI,0.5,04

value: Somatomotor cortex, left hemisphere


title: Transduced with DNAJB1::PRKACA sample 1

value: Primary human hepatocytes


title: PC9_3_NT1_1


title: Transduced with ATP1B1::PRKACA sample 3

value: Transduced with ATP1B1::PRKACA


title: H3K4me2, primary, REP2

value: lung carcinoma epithelial cells


title: 3xCHI,24,02

value: Female


title: PC9_Erlo_24h_1


title: PC9_3_DTEC_E_75_jours

value: erlotinib 1 uM, resistant proliferative clones


title: H3K4me2, primary, REP1


title: Transduced with an inactive DNAJB1::PRKACA sample 2


title: Transduced with ATP1B1::PRKACA sample 2


title: 3xCHI,4,01


title: Transduced with ATP1B1::PRKACA sample 1


title: H3K4me2, UI, REP2

value: UI


title: PC9_3_DTEC_D_75_jours

value: lung adenocarcinoma

value: epithelial cell


title: Transduced with DNAJB1::PRKACA sample 2


title: H3K4me2, UI, REP1


title: PC9_3_DTEC_B_75_jours

value: yes


title: C4_D16_3

city: Guangzhou

first: Cuihua

last: Wang

state: Guangdong

address: 601 Huangpu Ave, Guangzhou

institute: Guangzhou Lab

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the gencode (hg38_enst_v81) transcriptome using STAR (version 2.7)
The gene expression level was calculated by using  STAR
The RNA-seq data processing was performed as described. To analyze the regular gene expression, the reads were aligned to the reference transcriptome by RSEM and bowtie2 (—bowtie2— bowtie2-sensitivity-level very_sensitive —no-bam-output —estimate -rspd) using the index built by RSEM with the mouse genome, mm10, and Ensembl gene annotation track v74
Assembly: hg38
Supplementary files format and content: genes_cpm_expression

growth_protocol: H1 hESCs were subjected to EB-primed planar differentiatiation in defined cell culture conditions and in the absence of exogenous hematopoietic cytokines

extract_protocol:
total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Briefly, to induce hPSC differentiation, 1×106 single cells were spun at 100 × g for 4 minutes (min) into AggreWellTM400 (STEMCELL Technologies) in mTESR1 medium containing 1 μM Thiazovivin (GIBH CAS, China) and incubated for 24 hours at 37°C and 5% CO2. The newly formed clumps were placed on mCollagen IV (Corning Life Sciences, Bedford, MA)–coated surfaces in mTeSR1 medium supplemented with 4 ng/ml hrBMP4 (Peprotech, Rocky Hill, NJ), 50 ng/ml hrVEGF165 (Peprotech) and 10 μM Thiazovivin. After 48 hours, the medium was replaced with StemLineTM II medium (Sigma-Aldrich) supplemented with GlutaMAX®-I (Gibco®, ThermoFisher Scientific, Waltham, MA), 1 × NEAA (Gibco®), 50 µM 2-Mercaptoethanol (Sigma-Aldrich), 50 ng/ml hVEGF165 (Peprotech) and 6 μM SB-431542 (Tocris Bioscience, Bristol, UK). Forty-eight hours later, SB-431542 was removed from the medium. Onward, half of the medium, 2 mL in each well, was replaced with the fresh medium every second day until cell sorting. On Day 12, CD34+ cells were purified by MACS as described above and subjected to the T cell differentiation

tag: time point

value: embryonic stem cells

value: KO

value: blood differentiation


title: PC9_3_DTEC_A_75_jours


title: AstroP2Y1OE_3

city: Chuo

first: Eiji

last: Shigetomi

state: Yamanashi

address: 1110 Shimokato

institute: University of Yamanashi

data_processing:
Data filtering The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com/).
Structure variation detection The clean reads were mapped to the reference genome using HISAT2. After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to detect fusion genes and differential splicing genes (DSGs), respectively.
Expression level of gene was calculated by RSEM (v1.3.1). The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5).
Assembly: mm10
Supplementary files format and content: tab-delimitated text file includes raw read and FPKM

source_name: Hippocampus

extract_protocol:
RNA was harvested usin RNeasy Lipid Tissue Mini Kit (Qiagen)
RNA libraries for RNA-seq were prepared using vazyme TruePrep DNA Library Prep Kit following manufacturer’s protocol. 1 ng of total RNA was used for the construction of sequencing libraries.

value: Hippocampus

value: Astrocyte


title: HCC827Untreated3

value: DMSO


title: C4_D16_2


title: C4_D16_1


title: AstroP2Y1OE_2


title: wuxiaoqun_cDNA

city: Zhongshan

first: Xiuqiong

last: Xia

address: No. 2 Sunwen East Road, Zhongshan City, Guangdong Province

institute: Zhongshan People's Hospital

data_processing:
according to the automatic annotation results from singR and present them in barplot form using ggplot2 (version 3.3.5).
Assembly: GRCh38
Supplementary files format and content: A total of 58810 single cells were analyzed, including 38,244 cells from 4 samples without PDL1 expression, 14231 cells from 2 samples with PDL1 expression, and 6335 cells from 2 samples with high PDL1 expression.

source_name: lung cancer tissue,pT1cN0M0

extract_protocol:
Calculate the proportions of cell types in individual samples (above), different groups (bottom), immune/stromal cell (left) and total cell (right)
we collected eight tumor samples from eight lung cancer patients for scRNA-seq and bioinformatics analysis.

value: left upper lung

tag: library type

value: cDNA


title: wuxiaoqun_oligo

source_name: lung cancer tissue,pT1cN0M0,oligo

value: oligo


title: lijianming_cDNA

source_name: lung cancer tissue,pT2aN0M0

value: right lower lung


title: linyushen_oligo

source_name: lung cancer tissue,pT3N0M0,oligo

value: left lower lung


title: HCC827Untreated1


title: C4_D12_2


title: Ctrl_3

value: Ctrl


title: C4_D12_3


title: lijianming_oligo

source_name: lung cancer tissue,pT2aN0M0,oligo


title: HCC827Osimertinib11d3

value: osimertinib 1 uM, 11 days


title: C4_D12_1


title: HCC827Osimertinib11d2


title: Ctrl_1


title: Ctrl_2


title: C4_D9_3


title: zhongximei_oligo


title: C4_D9_2


title: zhongximei_cDNA


title: KO-PD1-E4

first: Jiqi

last: Shan

address: 1 Jianshe East Road, Erqi District, Zhengzhou City, Henan Province

institute: The First Affiliated Hospital of Zhengzhou University, Zhengzhou,

data_processing:
Reads were processed using 10X Genomics CellRanger V6.0
Assembly: mm10
Supplementary files format and content: processed gene-cell counts matrix in txt format

source_name: B16 Tumor

extract_protocol:
Cells were extracted according to 10X Genomics compatible protocol. Details can be found in the manuscript.
10X Genomics 3' Kit V2

value: B16 Tumor

value: T cell

value: anti-PD-1 antibody


title: wenweiming_oligo


title: HCC827Untreated2

value: lung adenocarcinoma

value: epithelial cell

value: yes


title: wenweiming_cDNA


title: KO-PD1-E3


title: AstroP2Y1OE_1


title: H4006_Erlo_DTEC_2

value: erlotinib 1 uM, resistant proliferative clones


title: C4_D9_1

value: embryonic stem cells

value: KO

value: blood differentiation


title: cuihuiwen_oligo

source_name: lung cancer tissue,pT1bN0M0,oligo

value: right upper lung


title: H3K4me3, UI, REP1

value: lung carcinoma epithelial cells

value: ChIP-grade Diagenode C15410003

value: UI


title: KO-PD1-E2


title: C4_D6_3


title: linyushen_cDNA

source_name: lung cancer tissue,pT3N0M0

value: left lower lung

value: cDNA


title: H4006_Erlo_DTC_3

value: erlotinib 1 uM, 21 days


title: cuihuiwen_cDNA

source_name: lung cancer tissue,pT1bN0M0


title: C4_D6_1


title: WT-PD1-E4

value: B16 Tumor


title: KO-PD1-E1

value: T cell


title: C4_D6_2


title: HCC827Osimertinib11d1

value: osimertinib 1 uM, 11 days


title: H4006_Erlo_DTC_2

value: lung adenocarcinoma


title: WT-PD1-E3

value: anti-PD-1 antibody


title: hurunzhong_oligo

source_name: lung cancer tissue,pT3NxM0,oligo

value: oligo


title: hurunzhong_cDNA

source_name: lung cancer tissue,pT3NxM0


title: H4006_Erlo_DTC_1

source_name: lung adenocarcinoma

value: epithelial cell

value: yes


title: 38_D16_2

value: embryonic stem cells

value: KO


title: H4006_Erlo_DTEC_3

value: erlotinib 1 uM, resistant proliferative clones


title: 38_D16_3

value: blood differentiation


title: chenfuran_oligo

source_name: lung cancer tissue,pT1cN2M0,oligo

value: right upper lung


title: WT-PD1-E2


title: H4006_Erlo_24h_3

value: erlotinib 1 uM, 24h


title: 38_D16_1


title: chenfuran_cDNA

source_name: lung cancer tissue,pT1cN2M0


title: H4006_Erlo_24h_2


title: H4006_Erlo_DTEC_1


title: 38_D12_3


title: H4006_Erlo_24h_1


title: snRNA_seq_BCAS_2

first: Yuan

last: Zhang

state: Shanghai

address: 130 Dong an Road, Shanghai 200032, China

institute: Fudan University

data_processing:
10X Genomics CellRanger (version 6.1.2)
Seurat
Assembly: mm10
Supplementary files format and content: snRNA-seq:raw feature matrix in Hierarchical Data Format format

source_name: brain; right cortex

growth_protocol: All the mice were housed in IVCs (Individually VentilatedCages) under SPF (Specific Pathogen Free) conditions, with sterile water and food ad libitum on a 12-h dark/light cycle.

extract_protocol:
In this study, for each library, the two right cortices from two mice in the same group were dissected and pooled together for the further nuclei suspension. preparation. After washed by cold 1x PBS, the brain tissue was transferred into the dounce homogenizer containing 5 ml of lysis buffer. After 20 times of up-and-down manual strokes on ice, the homogenized sample was transferred into a new 15 ml conical tube, followed by the centrifugation (4000 r.p.m., 4℃，5min). After centrifugation, the supernatant was discarded, and the precipitation (nuclei pellet) was retained. Then, the 15 ml tube was added with 1 ml of lysis buffer, and the nuclei pellet was pipetted by using a sterile 1 ml pipette tip until the nuclei were well distributed. After the nuclei suspension was added with 4 ml of lysis buffer and 5 ml of sucrose solution sequentially, the nuclei suspension was mixed well by gently inverting the tube ten times. After the centrifugation again (4000 r.p.m., 4℃，5min), the supernatant was discarded, and the precipitation (nuclei pellet) was retained. After the nuclei pellet was resuspended in 1 ml of FBS buffer, the nuclei pellet was pipetted by 1 ml and 200 μl pipette tip until the nuclei were well distributed. After 500 μl of nuclei suspension was taken for being filtered through a 40 μm cell strainer, the nuclei suspension were added 4 ml of FBS buffer. After the first nuclei count, all the nuclei solution was adjusted to a final concentration of 500-1200/μl.
The single-nuclei RNA-seq libraries were prepared using Chromium Single Cell 3ʹ Reagent Kits v3 from 10x Genomics  Single nuclei RNA-seq was performed on DNBSEQ-T7.

treatment_protocol:
The control group was exposed to sham operation
The experimental group was exposed to bilateral carotid artery stenosis (BCAS) operation

value: brain; right cortex

value: WT

tag: time

value: 14 weeks


title: 38_D12_2


title: snRNA_seq_BCAS_1

tag: tissue

value: bilateral carotid artery stenosis (BCAS) operation


title: H4006_CT_24h_3

tag: cell line

value: DMSO


title: H4006_CT_24h_2

tag: cell type